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Updated: Jun 8, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Chemical probing of RNA and RNA/protein complexes
1Department of Biology, University of Rochester, Rochester, New York, USA.
Abstract:
Chemical probing is widely used as a rapid approach for assessing RNA structure, folding, and function. In this chapter, we outline procedures for handling and using chemicals commonly used to probe nucleic acids. Detailed experimental conditions and design for footprinting and modification interference are presented herein. Protocols for RNA extraction, normalization, primer extension, and data evaluation are also provided. The methods described are designed to aid in the study of large RNAs, but with slight modifications are applicable to smaller RNAs.
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